New components of the spliced leader RNP required for nematode trans-splicing

Denker, John A.; Zuckerman, David M.; Maroney, Patricia A.; Nilsen, Timothy W.

doi:10.1038/nature00783

Cited by 50 publications

(42 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The SL RNA is transcribed from the intragenic spacer by RNA polymerase II, resulting in a pre-RNA which contains the SL sequence at its 5′ end, and binding sites for various components of the splicing machinery in its 3′ end [9,10]. The SL sequence is then removed from the nascent SL transcript and is trans-spliced on to the 5′ end of the nascent mRNA, through a biochemical pathway that bears many similarities to the cis-splicing pathway [11], although certain proteins have been shown to be specifically required for trans-splicing [10,11] In vitro biochemical systems employing nuclear extracts have been used to extensively dissect the trans-splicing pathway in the intestinal parasite Ascaris suum [7,[10][11][12][13]. These studies have resulted in the identification of a number of factors that are involved in the trans-splicing process [9][10][11] and have also succeeded in identifying the structural factors in the SL pre-RNA that are necessary for correct processing of the nascent transcript [7].…”

Section: Introductionmentioning

confidence: 99%

Sequences necessary for trans-splicing in transiently transfected Brugia malayi

Liu

Oliveira

Higazi

et al. 2007

Molecular and Biochemical Parasitology

View full text Add to dashboard Cite

Many genes in parasitic nematodes are both cis-and trans-spliced. Previous studies have demonstrated that a 7nt element encoded in the first intron of the B. malayi 70 kDa heat shock protein (BmHSP70) gene was necessary to permit trans-splicing of transgenic mRNAs in embryos transfected with constructs encoding portions of the BmHSP70 gene. Here we demonstrate that this element (the B. malayi HSP70 trans-splicing motif, or BmHSP70 TSM) is necessary and sufficient to direct trans-splicing of transgenic mRNAs derived from two genes naturally containing this motif. Mutations introduced into any position of the BmHSP70 TSM abrogated its ability to direct trans-splicing. Transgenic mRNAs derived from embryos transfected with constructs containing promoters and associated downstream domains from two normally trans-spliced genes that lack a BmHSP70 TSM homologue (the B. malayi 12 kDa small subunit ribosomal protein (BmRPS12) gene and the B. malayi RNA binding protein (BmRBP1) gene), were not trans-spliced. Transfer of the BmHSP70 TSM into the first intron of the BmRPS12 gene rendered it competent for trans-splicing. Insertion of the BmHSP70 TSM into the single intron of the BmRBP1 gene did not render it transsplicing competent. However, tagged constructs of the full-length BmRBP1 gene were trans-splicing competent. An analysis of the first exons and introns of over 200 trans-spliced B. malayi genes found homologues for the BmHSP70 TSM in roughly 25%. Thus, while the BmHSP70 TSM is necessary and sufficient to direct trans-splicing in some genomic contexts, independent trans-splicing signals are employed by other genes.

show abstract

Section: Introductionmentioning

confidence: 99%

Sequences necessary for trans-splicing in transiently transfected Brugia malayi

Liu

Oliveira

Higazi

et al. 2007

Molecular and Biochemical Parasitology

View full text Add to dashboard Cite

show abstract

“…SL RNAs are bound to the Sm proteins that are also core proteins in spliceosomal U1, U2, U4, and U5 snRNPs (Bruzik et al 1988; Thomas et al 1988;Van Doren and Hirsh 1988). In addition to the Sm proteins, the SL snRNP from Ascaris, a nematode that is distantly related to C. elegans, contains two novel proteins of 95 kDa (SL95p) and 30 kDa (SL30p) (Denker et al 1996(Denker et al , 2002. SL30p interacts with the splicing protein SF1/BBP that binds to the branchpoint.…”

Section: Introductionmentioning

confidence: 99%

A novel family of C. elegans snRNPs contains proteins associated with trans-splicing

MacMorris

Kumar

Lasda

et al. 2007

RNA

View full text Add to dashboard Cite

In many Caenorhabditis elegans pre-mRNAs, the RNA sequence between the 59 cap and the first 39 splice site is replaced by trans-splicing a short spliced leader (SL) from the Sm snRNP, SL1. C. elegans also utilizes a similar Sm snRNP, SL2, to trans-splice at sites between genes in polycistronic pre-mRNAs from operons. How do SL1 and SL2 snRNPs function in different contexts? Here we show that the SL1 snRNP contains a complex of SL75p and SL21p, which are homologs of novel proteins previously reported in the Ascaris SL snRNP. Interestingly, we show that the SL2 snRNP does not contain these proteins. However, SL75p and SL26p, a paralog of SL21p, are components of another Sm snRNP that contains a novel snRNA species, Sm Y. Knockdown of SL75p is lethal. However, knockdown of either SL21p or SL26p alone leads to cold-sensitive sterility, whereas knockdown of both SL21p and SL26p is lethal. This suggests that these two proteins have overlapping functions even though they are associated with different classes of snRNP. These phenotypic relationships, along with the association of SL26p with SL75p, imply that, like the SL1 RNA/Sm/SL75p/SL21p complex, the Sm Y/Sm/SL75p/SL26p complex is associated with trans-splicing.

show abstract

“…Indeed, the sequence looks like the AU-rich motif bound by AREbinding proteins. However, to date, no SL2-specific proteins have been identified, and the homologs of the transsplicing-specific proteins identified in Ascaris (Denker et al 2002) have been found on SL1 but not SL2 in C. elegans (MacMorris et al 2007). Finally, many mutations that fortuitously reduced the proposed base-pairing interfered with SL2 trans-splicing (Huang et al 2001).…”

Section: The Uayyuu Motif Of the Ur Elementmentioning

confidence: 99%

Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing

Lasda

Allen²,

Blumenthal³

2010

Genes Dev.

View full text Add to dashboard Cite

Spliced leader (SL) trans-splicing in Caenorhabditis elegans attaches a 22-nucleotide (nt) exon onto the 59 end of many mRNAs. A particular class of SL, SL2, splices mRNAs of downstream operon genes. Here we use an embryonic extract-based in vitro splicing system to show that SL2 specificity information is encoded within the polycistronic pre-mRNA, and that trans-splicing specificity is recapitulated in vitro. We define an RNA sequence required for SL2 trans-splicing, the U-rich (Ur) element, through mutational analysis and bioinformatics as a short stem-loop followed by a sequence motif, UAYYUU, located~50 nt upstream of the trans-splice site. Furthermore, this element is predicted in intercistronic regions of numerous operons of C. elegans and other species that use SL2 trans-splicing. We propose that the UAYYUU motif hybridizes with the 59 splice site on the SL2 RNA to recruit the SL to the pre-mRNA. In this way, the UAYYUU motif in the pre-mRNA would serve an analogous function to the similar sequence in the U1 snRNA, which binds to the 59 splice site of introns, effectively reversing the roles of snRNP and pre-mRNA in trans-splicing. In spliced leader (SL) trans-splicing, a short leader sequence is transferred from the 59 end of an SL RNA onto the first exon of a pre-mRNA (for review, see Nilsen 1993;Blumenthal 2005;Hastings 2005). This joins two discontinuous RNA sequences, and provides a common 59 sequence to many mRNAs. SL trans-splicing was identified first in trypanosomes and subsequently in numerous other organisms, ranging from protists to primitive chordates, and including roundworms, flatworms, arthropods, and cnidarians. However, it is not found in plants, A different form of trans-splicing has been reported in flies (Mongelard et al. 2002), and also recently in worms (Fischer et al. 2008). In these instances, exons of separate pre-mRNAs, neither one an SL RNA, are spliced together to form a mature mRNA containing portions of both premRNAs. Additionally, there have been numerous reports of a similar process in mammalian cells (Akiva et al. 2006) and plants (Zhang et al. 2010), where normally separate mRNAs are ''accidentally'' trans-spliced together. This sort of splicing has been implicated recently in cancers associated with translocations (Li et al. 2008).SL trans-splicing and cis-splicing (intron removal) are similar, and trans-splicing likely evolved from cis-splicing (Blumenthal 2004(Blumenthal , 2005. The splice site on the SL RNA closely matches the 59 splice site (59ss) consensus sequence, and the trans-splice site of the pre-mRNA has the same consensus sequence as intronic 39ss (Kent and Zahler 2000;Blumenthal 2005). In Caenorhabditis elegans, trans-splicing is signaled by a 39ss without an upstream 59ss. Artificial trans-splice sites can be created from cis-splice sites by removing an upstream 59ss (Conrad et al. 1991(Conrad et al. , 1995Maroney et al. 2000;Boukis and Bruzik 2001), and a trans-splice site can be made to cis-splice instead by insertion of a 59ss into the outron, the intr...

show abstract

New components of the spliced leader RNP required for nematode trans-splicing

Cited by 50 publications

References 15 publications

Sequences necessary for trans-splicing in transiently transfected Brugia malayi

Sequences necessary for trans-splicing in transiently transfected Brugia malayi

A novel family of C. elegans snRNPs contains proteins associated with trans-splicing

Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing

Contact Info

Product

Resources

About